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Bio::AlignIO::maf.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::AlignIO::maf - Multiple Alignment Format sequence input streamSYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class. use Bio::AlignIO; my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf'); while(my $aln = $alignio->next_aln()){ my $match_line = $aln->match_line; print $aln, "\n"; print $aln->length, "\n"; print $aln->no_residues, "\n"; print $aln->is_flush, "\n"; print $aln->no_sequences, "\n"; $aln->splice_by_seq_pos(1); print $aln->consensus_string(60), "\n"; print $aln->get_seq_by_pos(1)->seq, "\n"; print $aln->match_line(), "\n"; print "\n"; }
DESCRIPTION
This class constructs Bio::SimpleAlign objects from an MAF-format multiple alignment file.Writing in MAF format is currently unimplemented.
Spec of MAF format is here:
http://genome.ucsc.edu/FAQ/FAQformat
FEEDBACK
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:http://bugzilla.open-bio.org/
AUTHORS - Allen Day
Email: allenday@ucla.eduAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : my $alignio = Bio::AlignIO->new(-format => 'maf' -file => '>file', -idlength => 10, -idlinebreak => 1); Function: Initialize a new L<Bio::AlignIO::maf> reader Returns : L<Bio::AlignIO> object Args :
next_aln
Title : next_aln Usage : $aln = $stream->next_aln() Function: returns the next alignment in the stream. Throws an exception if trying to read in PHYLIP sequential format. Returns : L<Bio::SimpleAlign> object Args :
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